Variant report

Variant	rs12363350
Chromosome Location	chr11:57845321-57845322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10750876	0.82[CEU][hapmap];0.81[CHD][hapmap]
rs10750878	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.90[TSI][hapmap]
rs10750880	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10750881	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10750882	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs10750883	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10792130	0.89[GIH][hapmap]
rs10792133	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10896696	0.94[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10896705	0.83[JPT][hapmap]
rs11229247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs1123307	0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12226617	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1447168	0.82[CHB][hapmap]
rs1447169	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1451326	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs1868043	0.94[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.87[TSI][hapmap]
rs2003375	0.94[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2044856	0.83[CHB][hapmap]
rs2167358	0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2441979	0.91[GIH][hapmap]
rs2513726	0.89[GIH][hapmap]
rs2513727	0.89[GIH][hapmap]
rs2514187	0.87[GIH][hapmap]
rs3853677	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3974323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4939176	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4939182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6591455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7109726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7110748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7117711	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7118536	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.90[TSI][hapmap]
rs716945	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs921133	0.88[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap]
rs921134	0.89[GIH][hapmap]
rs921135	0.89[GIH][hapmap]
rs976429	0.94[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs976430	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv832165	chr11:57806024-58009076	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv523101	chr11:57843506-57871866	Enhancers Weak transcription	TF binding region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12363350	OR4C6	cis	parietal	SCAN
rs12363350	MS4A8B	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57840800-57847200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:57844000-57846800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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